PIPseq single cell

Illumina Single Cell 3′ RNA Prep (PIPseq) uses Particle‑templated Instant Partitions (PIPs) to create microfluidics‑free emulsions that barcode individual cells or nuclei. The workflow yields Illumina‑compatible 3′ gene expression libraries.

NXTGNT offers end‑to‑end support from cell or nuclei suspensions to sequencing and analysis:

  • 3′ Gene Expression from cells or nuclei
  • Optional cell‑surface protein using the SEA tag add‑on
  • Optional CRISPR guide capture
  • Scalable kit formats to profile thousands to tens of thousands of cells
  • Analysis with the DRAGEN PIPseq scRNA pipeline

 

How it works

 

Cells or nuclei are combined with barcoded template particles to form PIPs by simple mixing. Inside each emulsion droplet, mRNA is captured and barcoded. Pooled cDNA is processed into sequencing‑ready libraries. After sequencing on Illumina instruments, reads are assigned back to individual cells using the cell barcodes.

 

Illumina supplies the SEA kit to enrich synthetic nucleotide tags and supports workflows that use third-party antibody barcodes such as BioLegend TotalSeq. For PIPseq, you provide poly(A)-tailed antibody tags and run SEA to build the small feature library. For protein tagging, order BioLegend TotalSeq-A (poly A for poly dT capture) together with the Illumina SEA kit.

Applications

  • High‑throughput transcriptional profiling of complex tissues
  • Immune profiling with protein markers (SEA tags)
  • CRISPR perturbation screens

 

Deliverables

  • Demultiplexed FASTQ files
  • Counts matrix and QC metrics (DRAGEN PIPseq scRNA)
  • Optional: downstream Seurat/Scanpy objects on request

 

For more information, please do not hesitate to contact us directly.

Address

NXTGNT
Ghent University,
Faculty of Pharmaceutical Sciences
Ottergemsesteenweg 460
B-9000 Gent
Belgium

 

Inside the building

When entering the Ghent University Faculty of Pharmaceutical Sciences through the main entrance, elevators will be located in front of you. NXTGNT is situated on the third floor. When exiting the elevators, NXTGNT is located at your right-hand side.

 

Contact us

nxtgnt@UGent.be

Call: +32 9 264 80 59